Molecular Ecology Resources最新文献

{"title":"A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots","authors":"Jesse Erens,&nbsp;Christopher Heine,&nbsp;Stefan Lötters,&nbsp;Henrik Krehenwinkel,&nbsp;Andrew J. Crawford,&nbsp;Luis Alberto Rueda-Solano,&nbsp;Amadeus Plewnia","doi":"10.1111/1755-0998.70122","DOIUrl":"10.1111/1755-0998.70122","url":null,"abstract":"<p>Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase Amplification (RPA) and Oxford Nanopore sequencing, we introduce a two-step approach that uses non-invasive species barcoding to directly generate reference sequences for use in environmental DNA (eDNA) metabarcoding, and enables real-time, PCR-free and cost-effective molecular assessment of ecological communities in the field. Using an endemic and understudied tropical amphibian assemblage as a model, we demonstrate the functionality of this novel workflow. De novo generation of a reference sequence library from amphibian skin swab samples significantly improved the accuracy and taxonomic resolution of sequence assignments from eDNA samples, particularly on the species level, in turn allowing a characterisation of fine-scale patterns in community composition. Beyond generating new RPA-compatible amphibian metabarcoding primers, our results show that combining field-based eDNA metabarcoding with the offline assembly of a local reference database can directly bridge existing data gaps in molecular biodiversity monitoring, providing a scalable solution to accelerate biodiversity assessments in data-deficient ecosystems. This workflow paves the way for broader deployment of molecular tools in global biodiversity hotspots—particularly in remote and resource-limited tropical regions—to directly contribute critical baseline data, and support conservation efforts in regions where they are most urgently needed.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13036477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147579967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment","authors":"Luke J. McCartin,&nbsp;Samuel A. Vohsen,&nbsp;Annemarie L. Wood,&nbsp;Jeremy Horowitz,&nbsp;José J. Orozco-Juarbe,&nbsp;Nicole Pittoors,&nbsp;Declan Morrissey,&nbsp;Claudia F. Vaga,&nbsp;Colleen M. Hansel,&nbsp;Allen G. Collins,&nbsp;Andrea M. Quattrini,&nbsp;Santiago Herrera","doi":"10.1111/1755-0998.70130","DOIUrl":"10.1111/1755-0998.70130","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded <i>28S</i> barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic <i>28S</i> lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic <i>28S</i> lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13028928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147525115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GT-Seq Panel Development for Species Identification and Parentage Analysis of Closely Related Hybridising Scaphirhynchus Sturgeons","authors":"Junman Huang,&nbsp;Richard Flamio Jr.,&nbsp;Nathan R. Campbell,&nbsp;Aaron J. DeLonay,&nbsp;Amy C. Buhman,&nbsp;Edward J. Heist","doi":"10.1111/1755-0998.70124","DOIUrl":"10.1111/1755-0998.70124","url":null,"abstract":"<p>Hatchery supplementation is vital for conserving dwindling fish populations. Effective augmentation requires distinguishing hatchery-origin from wild individuals and accurately identifying species, particularly in systems where closely related species coexist. Genetic monitoring is key to quantifying genetic differences, but conventional markers do not distinguish hybrids, especially backcrosses. Misidentifying hybrids in hatchery programs compromises wild gene pools because hatchery broodstock contributes to numerous offspring being released into the wild. Here, we present a workflow for developing and evaluating the Genotyping-in-Thousands by sequencing (GT-seq) single nucleotide polymorphism (SNP) panel for North American river sturgeons (<i>Scaphirhynchus</i> spp.). This panel is designed to detect complex hybrid classes and to determine parent-offspring relationships. Our species identification panel (S-loci) contains 155 SNPs selected for high genetic differentiation (F_ST) between Pallid Sturgeon (<i>S. albus</i>) and Shovelnose Sturgeon (<i>S. platorynchus</i>), and the parentage assignment panel (P-loci) includes 112 SNPs with high heterozygosity within Pallid Sturgeon. Simulation analyses demonstrated that our GT-seq S-loci panel reliably classifies pure species, F1, F2 and backcross hybrids, even with up to 70% missing data. The P-loci panel achieves high-confidence parentage assignment with ≥ 80% typed loci, with performance influenced by the proportion of sampled parents. Overall, the novel <i>Scaphirhynchus</i> GT-seq panel developed in this study represents a robust and efficient tool for detecting hybridisation, assigning parentage and providing critical information for management decisions in ongoing Pallid Sturgeon conservation.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13031409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147525091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment","authors":"Alice Tagliabue,&nbsp;Giulia Furfaro,&nbsp;Alberto Pallavicini,&nbsp;Francesco Martino,&nbsp;Lorenzo Zane,&nbsp;Eleonora Sattin,&nbsp;Giorgio Valle,&nbsp;Stefano Piraino,&nbsp;Xavier Turon","doi":"10.1111/1755-0998.70126","DOIUrl":"10.1111/1755-0998.70126","url":null,"abstract":"<p>This study investigates the metazoan biodiversity in the Southern Adriatic Sea using environmental DNA (eDNA) metabarcoding. Sediment and adjacent water samples were collected from three sites (one pristine, two impacted by human activities) at three distances from the coast across two seasons. The complex four-factor experimental design (576 samples) addresses key sources of eDNA variability and provides a valuable comparison of markers (COI and 18S) and sample types, which remain rare in the literature. Results showed differences in the number and type of taxa identified, taxonomic resolution, and number of amplicon sequence variants (ASV) per operational taxonomic unit (OTU) across markers. The obtained overall community structure (beta-diversity) was similar for both markers. Sediment samples had higher OTU richness, but lower diversity than water samples. The two sample types provided distinct and only partially overlapping views of biodiversity. Sediment samples were rich in benthic species, whereas water samples featured mostly planktonic and nektonic species. Biodiversity varied by site and season, with sediment samples showing less seasonal variability. The pristine site did not host higher biodiversity than impacted sites, likely because of the latter's habitat heterogeneity. This study confirms the effectiveness of eDNA metabarcoding for biodiversity assessment in coastal ecosystems and provides a foundational dataset for future monitoring. By highlighting the complementary nature of COI and 18S markers and the role of sample type, this research supports integrating eDNA metabarcoding into routine environmental monitoring programs while emphasising the need for further standardisation and improved reference databases.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13014062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147508252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Limitations of Common Molecular Markers in Fungal Biodiversity Analysis and the Benefits of Their Synergistic Use","authors":"Vasilii Shapkin,&nbsp;Tomáš Zelenka,&nbsp;Tomáš Větrovský,&nbsp;Martin Kostovčík,&nbsp;Ivana Eichlerová,&nbsp;Petr Kohout,&nbsp;Lucia Žifčáková,&nbsp;Jan Borovička,&nbsp;Michal Tomšovský,&nbsp;Slavomír Adamčík,&nbsp;Petr Baldrian,&nbsp;Miroslav Kolařík","doi":"10.1111/1755-0998.70123","DOIUrl":"10.1111/1755-0998.70123","url":null,"abstract":"<p>High-throughput sequencing of the Internal Transcribed Spacer (ITS) regions is the primary method for estimating fungal diversity from environmental DNA. However, reliance solely on ITS markers is complicated by its high variability in sequence length and the presence of multiple variants within a single genome, which can bias diversity estimates. This study compares the performance of the ITS1 and ITS2 molecular markers with five alternative markers targeting protein-coding genes using a defined mock community of 413 fungal species from 32 orders. We show that none of the markers provided a reliable estimate of fungal diversity and two failed to produce sufficient data. While the ITS2 marker showed the highest proportion of individual species detections at 75.3%, a multi-marker approach significantly improved this result. Combining the top three markers (ITS1, ITS2 and elongation factor 1-alpha gene) increased this number to 92.2%. This approach also provided a crucial corrective for relative sequence abundance (RSA) estimates, as combining markers helps to offset the individual biases of each of them resulting in a more balanced picture of the community composition. Although the ITS region remains a cornerstone in fungal metabarcoding studies, we recommend combining both ITS1 and ITS2 markers with at least one alternative DNA marker to achieve more accurate species richness and RSA estimates. The broader application of these alternative markers will depend on the continued development of comprehensive, curated reference databases.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13013093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147508216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna","authors":"Mieke van der Heyde,&nbsp;Michael Curran,&nbsp;Stephanie Floeckner,&nbsp;Paul Nevill,&nbsp;Nicole E. White,&nbsp;Andy D. Austin,&nbsp;Michelle T. Guzik","doi":"10.1111/1755-0998.70127","DOIUrl":"10.1111/1755-0998.70127","url":null,"abstract":"<p>Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13012589/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147508201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and Laboratory Validation of a Field-Deployable CRISPR-Cas12a eDNA Assay for Phylogeographic Lineage Detection in Arctic Char (Salvelinus alpinus)","authors":"Darren J. Walsh,&nbsp;Rosaleen Hynes,&nbsp;Weili Guo,&nbsp;Cliodhna Surgenor,&nbsp;Paulo A. Prodöhl,&nbsp;Anne Parle-McDermott","doi":"10.1111/1755-0998.70125","DOIUrl":"10.1111/1755-0998.70125","url":null,"abstract":"<p>Environmental DNA (eDNA) tools are increasingly used for biodiversity monitoring, with most existing assays targeting species-level identification. However, the use of eDNA to resolve intraspecific genetic variation remains rare and methodologically underdeveloped. This study presents the development and laboratory validation of a novel molecular assay capable of detecting specific phylogeographic lineages, advancing eDNA applications by enabling resolution below the species level. The assay combines Recombinase Polymerase Amplification (RPA) and CRISPR-Cas12a technologies with a lateral flow platform for field-ready, on-site detection. Irish Arctic char (<i>Salvelinus alpinus</i>) was selected as the model due to its conservation relevance and post-glacial lineage diversity in Ireland. Mitochondrial genome sequencing of known Irish lineages identified a Protospacer Adjacent Motif (PAM) site unique to the Atlantic Subclade 1 lineage, allowing clear discrimination from co-occurring lineages. Two assays were optimised: a species-specific assay detecting all Arctic char lineages and a lineage-specific assay targeting Lineage 1. Both showed high sensitivity and specificity under laboratory conditions, with LbCas12a outperforming AsCas12a at optimised buffer concentrations. The lateral flow adaptation, utilising a dual-labelled FAM-Biotin probe, enabled portable and rapid detection with minimal equipment. Field validation using eDNA from Irish lakes highlighted the need for improved sampling protocols, as lake-edge surface samples failed to yield detections. This assay represents the first reported example of a CRISPR-based eDNA tool for phylogeographic lineage detection in the field. It offers a novel, non-invasive, and scalable approach to fine-scale ecological monitoring and establishes a foundation for future conservation tools targeting intraspecific diversity.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13004180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data","authors":"Manon Mireille Geerts,&nbsp;Manuel Curto,&nbsp;Andrew J. Alverson,&nbsp;Jeffery Stone,&nbsp;Hugo F. Gante","doi":"10.1111/1755-0998.70128","DOIUrl":"10.1111/1755-0998.70128","url":null,"abstract":"<p>Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of <i>Stephanodiscus hantzschii</i> with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel <i>Cyclotella</i> plastome with only 94.0% identity to its closest available reference, <i>Cyclotella atomus</i>. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13003286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Genomics Provide Insights Into Karyotype Evolution in Vespertilionid Bats (Vespertilionidae, Chiroptera)","authors":"Linjing Lan,&nbsp;Xin Zhang,&nbsp;Jinjin Xie,&nbsp;Xiaohui Lin,&nbsp;Xihong Hong,&nbsp;Wenhui Nie,&nbsp;Jinhuan Wang,&nbsp;Weiting Su,&nbsp;Fengtang Yang,&nbsp;Guimei He,&nbsp;Xiuguang Mao","doi":"10.1111/1755-0998.70129","DOIUrl":"10.1111/1755-0998.70129","url":null,"abstract":"<p>Studies elucidating the molecular basis and evolutionary consequences of karyotypic changes in mammals remain scarce. Here, we investigate chromosomal evolution by focusing on two contrasting lineages within the family Vespertilionidae (Chiroptera): the karyotypically variable tribe Pipistrellini and the highly conserved genus <i>Myotis</i>. Pipistrellini exhibits extensive karyotype diversity, with diploid numbers (2n) ranging from 26 to 44, whereas <i>Myotis</i> demonstrates remarkable stability, maintaining 2n = 44 across nearly all studied species. To uncover the mechanisms driving these divergent evolutionary trajectories, we generated a high-quality chromosome-level genome assembly for <i>Pipistrellus abramus</i> (2n = 26). By integrating multiple high-quality vespertilionid genomes, we reconstructed the family phylogeny and inferred an ancestral karyotype of 2n = 44, revealing fusions and fissions as the primary drivers of karyotypic diversification. We further identified an enrichment of rolling-circle (RC) and recent DNA transposons in genes involved in DNA metabolism, suggesting a mechanistic basis for transposable element (TE) tolerance in Vespertilionidae. In <i>P. abramus</i>, a derived chromosome originated from three ancestral chromosomes via Robertsonian and end-to-end fusions, with TEs significantly enriched at fusion sites. Genome stability-related genes and contracted gene families also appear to facilitate adaptive responses to structural changes. These findings provide novel insights into the molecular mechanisms underlying chromosome evolution and speciation in mammals.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13003292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities","authors":"Olivier Morissette,&nbsp;Guillaume Côté,&nbsp;Marc-Antoine Couillard,&nbsp;Rémy Pouliot,&nbsp;Louis Bernatchez","doi":"10.1111/1755-0998.70131","DOIUrl":"10.1111/1755-0998.70131","url":null,"abstract":"<p>Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13003273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}